For me it stops at \newacronym{PIGK}{PIGK}{phosphatidylinositol glycan anchor biosynthesis class K}, having some higher main memory size, but it takes very long to get there
– user31729Feb 28 '18 at 22:50

Perhaps bib2gls is an option for you
– user31729Feb 28 '18 at 22:56

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You could perhaps use lualatex which uses dynamic memory allocation but it's very big (my texlive 2017 version finally dies with ! TeX capacity exceeded, sorry [number of strings=494451]., I would instead just get latex to write out which acronyms are used, then use perl to make a subset list of definitions to input.
– David CarlisleFeb 28 '18 at 22:57

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@tommy.carstensen if you posted a test file it would be easier to suggest how to get there
– David CarlisleFeb 28 '18 at 22:59

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@tommy.carstensen: I would rather split the huge file into more 'logical' files, e.g. a file containing some frequently used genes ...
– user31729Feb 28 '18 at 23:09

The glossaries performance page compares the results of document builds for some files containing 1000 entry definitions, using a number of different methods provided by the base glossaries package and the glossaries-extra extension package. In particular, check the Alphabetical Order (Subset) section. The files in these tests aren't as large as with your document, but it's possible to see which methods perform better for large datasets.

The best method for a large set of entries where only a subset is required in the document is to use glossaries-extra with bib2gls. This has a considerable saving in resources as only those entries that are actually needed in the document require storage within TeX. (Naturally, bib2gls will need enough memory, but it's a Java application so it has better memory management than TeX.)

Thanks! I would probably have gone for bib2gls, if I had to do it again, instead of pruning the glossary of human gene IDs.
– tommy.carstensenMar 2 '18 at 16:54

@tommy.carstensen You might be able to convert your .tex file to .bib format with convertgls2bib. (One drawback is that bib2gls is quite new, so there may be bugs that haven't been found yet.)
– Nicola TalbotMar 2 '18 at 17:03